Technical Field
The present disclosure relates to methods, arrays and kits for assessing the quality of DNA samples.
Description of the Related Art
DNA has become biomarkers with the most potential. Compared to other biomarkers, DNA is stable and has less dynamic change. In addition, DNA as biomarkers is sequence based and has less ambiguity. Recently, discovery of DNA as biomarkers has been propelled by the growing application of next generation sequencing (NGS).
The quality of any scientific data is directly proportional to that of the starting samples. It is important to assess the quality of a starting DNA sample for downstream molecular analyses, such as qPCR assays and NGS. A bad quality sample will generate unusable data, which causes waste in material and labor. Not knowing the DNA quality can also lead to misuse of precious sample, which once used, cannot be recovered.
Various methods are known for DNA quality evaluation. Most commonly used spectrometrical methods can address some of the questions in DNA concentration and contaminants. However, it cannot detect many contaminants easily or evaluate the actual impact of contaminants in the molecular assays. Electrophoresis can evaluate the sizes of DNA sample. However, it cannot evaluate base damages, cross-linkage, modifications, which can adversely affect downstream enzymatic assays. Other people select to test a group of gene assays in PCR to estimate actual sample performance in molecular assays. However, selection of a few gene assays is sometimes biased, affected by biological changes in local chromosomal structure (as seen in pathological conditions) and does not have broader representations. Thus, the prediction for a performance of DNA samples in downstream molecular applications has been challenging, especially for DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Accordingly, there is a need to establish an objective method to evaluate the quality of DNA for downstream DNA analyses.